Without a doubt I say Amelia and the Doctor. I think that since he met her when she was a little girl and he was his 30's (or late 20's, I have no clue) it would make it a bit awkward. I think that her and Rory are great together though. He waited for her, and she pretty much died for him (I know she didn't ACTUALLY die, but in The Angels Take Manhattan it's pretty much dying). Besides (as much as I hate to say it), the Doctor didn't come back for her. She waited 12 years, probably crying her moyo out at how she was left behind kwa her Raggedy Man, not going away from her nyumbani where she was a little Scottish girl in a world where everyone was English. Rory was there for her, no matter if she forgot about him au anything. He was always there, going along with her obsession with the Raggedy Man and dealing with her talking about him all the time. He probably had to make dolls with her, all the while thinking that she would always like her imaginary friend zaidi than she liked him. He was waiting for her before the Pandorica. He waited for her his whole life. And that is why the Doctor isn't good with her. The Doctor arrived late, and Rory came early. wewe can't expect him to compete with that.
The Doctor. Definitely!! Have wewe seen the way they look at each other? Have wewe seen the way they hug? And the forehead kisses? I believe what they feel about each other is WAY zaidi THAN JUST FRIENDSHIP. They had a magical story and a wonderful time together. Remember that beautiful and sad episode, Vincent and The Doctor? It wouldn't have been the same if Rory was there. Amy and The Doctor are made for each other! But I looked at the majibu and seems like everyone thinks Rory is the one for her. Like, what??? Amy is constantly watching Rory die, and following him to death, how is that romantic au something? When they are getting divorced in Asylum of The Daleks he thinks he has the right to mock her just because she is a model. And wow, remember the "I upendo wewe zaidi than wewe upendo me"? hahahahah, yeah sure, Rory is the one for her. And I won't even mention how selfish he was for wanting Amy to grow up and give up that wonderful life she had with the doctor. Of course, didn't say it directly but he showed this feelings a lot. "It's Amy's dream too, isn't it Amy?" hahaha